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bio-alignment-indexing
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By BioTender-max/awesome-bio-agent-skills (GitHub) · design · 219 stars · scanned at commit 8cbdd18
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
Works with any agent that supports SKILL.md skills.
What this skill can do
Runs commands on your computer
The author does not mention this.
Found in 17 places.
Show 14 more
- skills/bioskills/alignment-indexing/SKILL.md, line 74
samtools index input.bam output.bai - skills/bioskills/alignment-indexing/SKILL.md, line 79
samtools index -@ 4 input.bam - skills/bioskills/alignment-indexing/SKILL.md, line 84
samtools index input.cram - skills/bioskills/alignment-indexing/SKILL.md, line 93
samtools view -H input.bam | grep "^@HD" - skills/bioskills/alignment-indexing/SKILL.md, line 110
samtools view input.bam chr1:1000000-2000000 - skills/bioskills/alignment-indexing/SKILL.md, line 115
samtools view input.bam chr1:1000-2000 chr2:3000-4000 - skills/bioskills/alignment-indexing/SKILL.md, line 120
samtools view -L regions.bed input.bam - skills/bioskills/alignment-indexing/SKILL.md, line 205
samtools idxstats input.bam - skills/bioskills/alignment-indexing/SKILL.md, line 223
samtools view -c -F 2304 input.bam chr1 # primary only - skills/bioskills/alignment-indexing/SKILL.md, line 228
samtools idxstats file.bam | awk '{sum+=$4} END {print sum}' # idxstats unmapped (sum across all rows; PE orphans get a contig RNAME) - skills/bioskills/alignment-indexing/SKILL.md, line 234
samtools idxstats input.bam | awk '{sum += $3} END {print sum}' - skills/bioskills/alignment-indexing/SKILL.md, line 249
samtools faidx reference.fa - skills/bioskills/alignment-indexing/SKILL.md, line 278
if [ input.bam -nt input.bam.bai ]; then - skills/bioskills/alignment-indexing/SKILL.md, line 288
samtools view -H input.bam | grep '^@SQ' | head -3
Connects to the internet
The author does not mention this.
Found in 9 places.
Show 6 more
- skills/bioskills/alignment-indexing/SKILL.md, line 183
for read in bam.fetch('chr1', 1000000, 1000001): - skills/bioskills/alignment-indexing/SKILL.md, line 259
seq = ref.fetch('chr1', 1000, 2000) - skills/bioskills/alignment-indexing/SKILL.md, line 269
| Fetch region | `samtools view file.bam chr1:1-1000` | `bam.fetch('chr1', 0, 1000)` | - skills/bioskills/alignment-indexing/examples/fetch_regions.py, line 24
for read in bam.fetch(chrom, start - 1, end): # Convert to 0-based - skills/bioskills/alignment-indexing/usage-guide.md, line 128
for read in bam.fetch('chr1', 1000000, 2000000): - skills/bioskills/alignment-indexing/usage-guide.md, line 151
seq = ref.fetch('chr1', 999, 2000) # 0-based coordinates
Downloads and installs other software
The author does not mention this.
Found in 1 place.
Safer alternatives
Low-risk skills in the same category (design) that look related. Check that one does what you need.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'bio-alignment-indexing' ] || [ -L ~/.agents/skills/'bio-alignment-indexing' ]; then echo 'A skill folder named bio-alignment-indexing already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/BioTender-max/awesome-bio-agent-skills' "$d" && git -C "$d" checkout --quiet '8cbdd18837aa6296c4e77616a03b323bd69b57b1' -- 'skills/bioskills/alignment-indexing' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bioskills/alignment-indexing' ~/.agents/skills/'bio-alignment-indexing' && rm -rf "$d"; fi
Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-alignment-indexing' ~/.claude/skills/'bio-alignment-indexing' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.
Badge for your README
The badge for BioTender-max/awesome-bio-agent-skills shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/BioTender-max/awesome-bio-agent-skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-07 | 8cbdd18 | 75 |